On Sun 14 Apr, 2019, 11:15 AM Ayesha Fatima, <ayeshafatima...@gmail.com> wrote:
> Dear All, > I have a glyceryl monooleate 100 molecule assembly. I want to pull a > peptide like molecule through it. I have obtained the forcefield files > from *Boeckmann, > Rainer website.* > I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but > got stuck as the force field obtained from Rainer website and put in the > working directory, the path to working directory does not appear in the > list of forcefields. > i prepared my molecule using 54a7 forcefield implemented in ATB server. i > got the itp files and prepared the gro file using editconf > My question is to anyone who has done the glycerol simulation using > gromacs. please help with the exact procedure to develop the simulation > files. Should I add the 54a7 forcefield with to the OPLSAA updated > forcefield by Prof Rainer or vice versa? I also have a peptide like > molecule to pull through the GMO membrane. Any one can help guide through > this? > Hi You must add the ff in Ur gromacs directory and not in Ur working directory. For example, use/local/gromacs/share/gromacs/top And that will reflect the FF in pdb2gmx. > > Thank you in anticipation > Ayesha > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.